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Is there a way to generate an empty (skeleton) SeqArray GDS ?
Cheers
Thierry
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Hi there,
I really love this package and I wrote one function to parse several type of VCF output (from several caller) into a standardised format with standardised columns (https://annaquaglieri1…
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Hi Devels,
Thank you for this library.
I'm interested to use this package to estimate threshold for a three-way admixed population: afr amer, native, and European in hispanics. I've very limited …
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One of my unit tests in SeqArray is now failing to read an example file:
```
vcffile
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Noticed this issue downstream of a GWAS analysis using the GENESIS package, but the remove.monosnp option of snpgdsLDpruning() seems to be ignoring heterozygote calls. Post LD prunning I am not encoun…
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```R
library(SeqArray)
f
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with the test dataset sent by email:
```
require(SNPRelate)
require(magrittr)
require(rlang)
data Working space: 50 samples, 782 SNVs
> using 1 (CPU) core
> sliding window: 500,000 bas…
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Is there a way to get (`SeqArray::seqGetData`) genotypes in the form of nucleotides, e.g. A/T
similar to `SeqVarTools::getGenotypeAlleles` ? The last one is very slow for big VCFs.
cheers
Thierry
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Hi Thierry,
I am attempting to use radiator::filter_rad to filter a populations.snps.vcf file from Stacks, but I am consistently getting an error in ''generating individual stats" and then I do not…
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Dear zhengxwen,
Thanks a lot for your great packages on variants. They are super fast and bring the world of PLINK into the R/Bioc universe.
I tried to seqMerge() two GDS files (origninally crea…